Spatiotemporal deciphering of dynamic the FUS interactome during liquid-liquid phase separation in living cells

Liquid-liquid phase separations (LLPS) are membraneless organelles driven by biomolecule assembly and are implicated in cellular physiological activities. However, spatiotemporal deciphering of the dynamic proteome in living cells during LLPS formation remains challenging. Here, we introduce the Composition of LLPS proteome Assembly by Proximity labeling-assisted Mass spectrometry (CLAPM). We demonstrate that CLAPM can instantaneously label and monitor the FUS interactome shifts within intracellular droplets undergoing spatiotemporal LLPS. We report 129, 182 and 822 proteins specifically present in the LLPS droplets of HeLa, HEK 293 T and neuronal cells respectively. CLAPM further categorizes spatiotemporal dynamic proteome in droplets for living neuronal cells and identifies 596 LLPS-aboriginal proteins, 226 LLPS-dependent proteins and 58 LLPS-sensitive proteins. For validation, we uncover 11 previously unknown LLPS proteins in vivo. CLAPM provides a versatile tool to decipher proteins involved in LLPS and enables the accurate characterization of dynamic proteome in living cells.